Problem with running turtorial of rna denovo

[Anonymous]

Hi,

I am a new user of rosetta and tried to run tutorials with rna denovo structure prediction. However, when I ran the tutorial, the program said it could not find the rna folder and the information is kept in coarse_rna fold. So I have to create a rna fold that link to coarse_rna fold. However, in that folder, it doesn’t have residue_types.txt which is hightlighted below. Could you help to solve my problem? Thank you very much.

My

 

$ rna_denovo.mpi.linuxgccrelease -native chunk002_1lnt_RNA.pdb  -fasta chunk002_1lnt_.fasta -nstruct 1 -out:file:silent chunk002_1lnt.out -cycles 1

000 -minimize_rna -filter_lores_base_pairs -output_lores_silent_file

Basic usage:  rna_denovo.mpi.linuxgccrelease  -fasta <fasta file with sequence>  [ -native <native pdb file> ]

 Type -help for full slate of options.

core.init: (0) Mini-Rosetta version Split from developer trunk at 53488 from http://www.rosettacommons.org

core.init: (0) command: rna_denovo.mpi.linuxgccrelease -native chunk002_1lnt_RNA.pdb -fasta chunk002_1lnt_.fasta -nstruct 1 -out:file:silent chunk002_1lnt.out -cycles 1000 -minimize_rna -filter_lores_base_pairs -output_lores_silent_file

core.init: (0) ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=1910561846 seed_offset=0 real_seed=1910561846

core.init.random: (0) RandomGenerator:init: Normal mode, seed=1910561846 RG_type=mt19937

core.init: (0) found database environment variable ROSETTA3_DB: /N/u/myle/Karst/rosetta/main/database

Warning: (0) Unable to locate database file chemical/residue_type_sets/rna

ERROR: Unable to open file: /N/u/myle/Karst/rosetta/main/database/chemical/residue_type_sets/rna/residue_types.txt

ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 110

terminate called after throwing an instance of ‘utility::EXCN_utility_exit’

[h1:21651] *** Process received signal ***

[h1:21651] Signal: Aborted (6)

[h1:21651] Signal code:  (-6)

[h1:21651] [ 0] /lib64/libpthread.so.0(+0xf7e0) [0x7f914a12a7e0]

[h1:21651] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x7f9149db9495]

[h1:21651] [ 2] /lib64/libc.so.6(abort+0x175) [0x7f9149dbac75]

[h1:21651] [ 3] /N/soft/rhel6/gcc/4.7.2/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x11d) [0x7f914a5acd6d]

[h1:21651] [ 4] /N/soft/rhel6/gcc/4.7.2/lib64/libstdc++.so.6(+0x5de66) [0x7f914a5aae66]

[h1:21651] [ 5] /N/soft/rhel6/gcc/4.7.2/lib64/libstdc++.so.6(+0x5de93) [0x7f914a5aae93]

[h1:21651] [ 6] /N/soft/rhel6/gcc/4.7.2/lib64/libstdc++.so.6(+0x5e0be) [0x7f914a5ab0be]

[h1:21651] [ 7] /N/soft/rhel6/rosetta/gnu/3.5/mpi/libutility.so(_ZN7utility4exitERKSsiS1_i+0xc7) [0x7f914cf94247]

[h1:21651] [ 8] /N/soft/rhel6/rosetta/gnu/3.5/mpi/libcore.2.so(_ZN4core8chemical14ResidueTypeSetC2ERKSsS3_RKSt6vectorISsSaISsEES8_+0x1ad8) [0x7f914dfe39e8]

[h1:21651] [ 9] /N/soft/rhel6/rosetta/gnu/3.5/mpi/libcore.2.so(_ZN4core8chemical15ChemicalManager16residue_type_setESs+0x4c4) [0x7f914df710f4]

[h1:21651] [10] rna_denovo.mpi.linuxgccrelease(_Z15rna_denovo_testv+0x3d) [0x41870d]

[h1:21651] [11] rna_denovo.mpi.linuxgccrelease(_Z7my_mainPv+0x9) [0x41aaf9]

[h1:21651] [12] rna_denovo.mpi.linuxgccrelease(main+0x1067) [0x434847]

[h1:21651] [13] /lib64/libc.so.6(__libc_start_main+0xfd) [0x7f9149da5d1d]

[h1:21651] [14] rna_denovo.mpi.linuxgccrelease() [0x4168d5]

[h1:21651] *** End of error message ***

Aborted

[Anonymous]

It looks like you’re using the executables from Rosetta 3.5  There’s been a *lot* of improvements to the RNA code since Rosetta 3.5 was released 4 years ago, so I’d highly recommend updating to a more recent version, if possible.

While you’re using the executables from Rosetta 3.5, it looks like your database (specified with the ROSETTA3_DB environment variable) is *not* for Rosetta 3.5. The version mismatch issue is also probably why you’re having troubles – different versions have slightly different layouts and contents in the database directory. You should always use the version of the database which comes with the version of the code you’re using.

Most recent versions of Rosetta can autodetermine the location of the database if you don’t move the binaries and database from where they are in the download hierarchy. As such, you can forgo passing the -database option, or setting the ROSETTA3_DB environment variable, and not have to worry about database version mismatches.  — The one trick is that Rosetta will obey the ROSETTA3_DB environment variable if set, so you might have to delete/disable that, if it’s pointing to the wrong version (this looks like it’s the case for you).

[Anonymous]

It looks like you’re using the executables from Rosetta 3.5  There’s been a *lot* of improvements to the RNA code since Rosetta 3.5 was released 4 years ago, so I’d highly recommend updating to a more recent version, if possible.

While you’re using the executables from Rosetta 3.5, it looks like your database (specified with the ROSETTA3_DB environment variable) is *not* for Rosetta 3.5. The version mismatch issue is also probably why you’re having troubles – different versions have slightly different layouts and contents in the database directory. You should always use the version of the database which comes with the version of the code you’re using.

Most recent versions of Rosetta can autodetermine the location of the database if you don’t move the binaries and database from where they are in the download hierarchy. As such, you can forgo passing the -database option, or setting the ROSETTA3_DB environment variable, and not have to worry about database version mismatches.  — The one trick is that Rosetta will obey the ROSETTA3_DB environment variable if set, so you might have to delete/disable that, if it’s pointing to the wrong version (this looks like it’s the case for you).

[Anonymous]

It looks like you’re using the executables from Rosetta 3.5  There’s been a *lot* of improvements to the RNA code since Rosetta 3.5 was released 4 years ago, so I’d highly recommend updating to a more recent version, if possible.

While you’re using the executables from Rosetta 3.5, it looks like your database (specified with the ROSETTA3_DB environment variable) is *not* for Rosetta 3.5. The version mismatch issue is also probably why you’re having troubles – different versions have slightly different layouts and contents in the database directory. You should always use the version of the database which comes with the version of the code you’re using.

Most recent versions of Rosetta can autodetermine the location of the database if you don’t move the binaries and database from where they are in the download hierarchy. As such, you can forgo passing the -database option, or setting the ROSETTA3_DB environment variable, and not have to worry about database version mismatches.  — The one trick is that Rosetta will obey the ROSETTA3_DB environment variable if set, so you might have to delete/disable that, if it’s pointing to the wrong version (this looks like it’s the case for you).

[Anonymous]

Thank you so much for your suggestion. I will ask the IT at my school to install the new Rosetta version then.

Best,

My

[Anonymous]

Thank you so much for your suggestion. I will ask the IT at my school to install the new Rosetta version then.

Best,

My

[Anonymous]

Thank you so much for your suggestion. I will ask the IT at my school to install the new Rosetta version then.

Best,

My

[Anonymous]

Note that if IT is being slow or hesitant about it, you don’t *need* to get them to install things centrally.  Rosetta is set up such that you should be able to download and compile it in a user directory, without any sort of administrator privileges. (Well, aside from any privileges needed to compile C++ programs, which most users should be able to do on most Unix-like computer systems, assuming a usable compiler is installed.) So you should be able to install whatever version of Rosetta you like to your home directory, and then run it from there.

[Anonymous]

Note that if IT is being slow or hesitant about it, you don’t *need* to get them to install things centrally.  Rosetta is set up such that you should be able to download and compile it in a user directory, without any sort of administrator privileges. (Well, aside from any privileges needed to compile C++ programs, which most users should be able to do on most Unix-like computer systems, assuming a usable compiler is installed.) So you should be able to install whatever version of Rosetta you like to your home directory, and then run it from there.

[Anonymous]

Note that if IT is being slow or hesitant about it, you don’t *need* to get them to install things centrally.  Rosetta is set up such that you should be able to download and compile it in a user directory, without any sort of administrator privileges. (Well, aside from any privileges needed to compile C++ programs, which most users should be able to do on most Unix-like computer systems, assuming a usable compiler is installed.) So you should be able to install whatever version of Rosetta you like to your home directory, and then run it from there.

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